Making Zalman 3D stereoscopic movie with Pymol

A crash course how to make a 3D-molecular movie. I am using Zalman ZM-M240W monitor with NVIDIA Quadro FX580 graphic card. You need the Zalman monitor and polarized glasses to see the 3D stereo. Only PyMOL 1.3 and any .png to .gif converter (eg. Adobe Image Ready) are required to make animation like this.

Here is the instruction.

  1. Open PyMOL> Stereo 3D Launch > Pymol Zalman 3D
  2. Once in PyMOL, File> Open> click on “filename.pse”
  3. PyMOL> stereo on (To trigger stereoscopic function for Zalman monitor)
  4. PyMOL> mset 1 x60 (To create movies with 60 frames)
  5. PyMOL> util.mroll 1,60 (To rotate molecules 360 degrees in 60 frames)
  6. PyMOL> set ray_trace_frames=1 (To make high quality pictures)
  7. PyMOL> mpng frame_ (This command will generate multiple files in MyDocuments folder with prefix frame_xxx.png)
  8. Then use Adobe ImageReady to put them into GIF by File> Import> Folder as frames> and click on the folder that contains frame_001.png, etc.
  9. Look at the animation with the “play” button
  10. Then click File>Save Optimizes As > “filename.gif”

Showing how various distances in the kinase pockets influences the Kd. The smaller Kd,STU requires longer orange bar, shorter purple bar, and optimal cyan bar. Google-chrome compatible, please click to see in high-resolution 3D movie.


Figure Reference:
Tanramluk D, Schreyer A, Pitt WR, Blundell TL (2009) On the origins of enzyme inhibitor selectivity and promiscuity: a case study of protein kinase binding to staurosporine. Chem Biol Drug Des 74(1): 16-24.



About nanonan

Bioinformaticist and Structural Biologist
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